[English] 日本語
Yorodumi- PDB-4uuw: Competence or damage-inducible protein CinA from Thermus thermophilus -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uuw | ||||||
---|---|---|---|---|---|---|---|
Title | Competence or damage-inducible protein CinA from Thermus thermophilus | ||||||
Components | CINA-LIKE PROTEIN | ||||||
Keywords | BIOSYNTHETIC PROTEIN / COMPETENCE / DAMAGE / NAD RECYCLING | ||||||
Function / homology | Function and homology information | ||||||
Biological species | THERMUS THERMOPHILUS HB8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Derrick, J. / Karuppiah, V. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Structure and Mechanism of the Bifunctional Cina Enzyme from Thermus Thermophilus Authors: Karuppiah, V. / Thistlethwaite, A. / Dajani, R. / Warwicker, J. / Derrick, J.P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4uuw.cif.gz | 171 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4uuw.ent.gz | 134.6 KB | Display | PDB format |
PDBx/mmJSON format | 4uuw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uu/4uuw ftp://data.pdbj.org/pub/pdb/validation_reports/uu/4uuw | HTTPS FTP |
---|
-Related structure data
Related structure data | 4ct8SC 4ctaC 4uocC 4uuxC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 43043.359 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMUS THERMOPHILUS HB8 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q5SHB0 |
---|
-Non-polymers , 5 types, 454 molecules
#2: Chemical | ChemComp-AMP / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 53 % / Description: NONE |
---|---|
Crystal grow | pH: 6.5 Details: 0.2 M NA2SO4, 0.1 M BIS-TRIS PROPANE (PH 6.5) AND 20% (WT/VOL) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→53 Å / Num. obs: 63973 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.98→2.03 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.3 / % possible all: 99.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CT8 Resolution: 1.98→52.94 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.772 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.477 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98→52.94 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|